Pharmacophore generation

This protocol generate a Pharmacophore object that can be parse by RDKit from a SetOfSmallMolecules. If the input molecules are docked to a structure, the output pharmacophore keeps that structure too. The different features that can be captured by the pharmacophore are defined in the BaseFeatures.def file of RDKit. scipion-chem uses the families of those features as own features (Donor, Acceptor, Hydrophobe, Aromatic…).

Different cluster parameters can be chosen to generate the pharmacophore, they control the clustering method and how conserved the feature must be among the docked small molecules.

Input

Note

All parameters include a help button that gives further information for each of them.

Pharmacophore generation form 1

Pharmacophore generation form 2

The result of this protocol is a PharmacophoreChem object containing the extracted features from the set of small molecules with the specified clustering parameters.

Pharmacophore generation output

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests pwchem.tests.tests_pharmacophores.TestPharmGeneration